Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of closely related citrus varieties

ABSTRACT: An experiment was performed to predict citrus varieties by means of supervised learning algorithms applied to gene expression profiles

ORGANISM(S): Citrus clementina

SUBMITTER: Jose Gadea

PROVIDER: E-TABM-76 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Class prediction of closely related plant varieties using gene expression profiling.

Ancillo G G Gadea J J Forment J J Guerri J J Navarro L L

Journal of experimental botany 20070423 8

In recent years, class prediction experiments have been largely developed in cancer research with the aim of classifying unknown samples by examining their expression signature. In natural populations, a significant component of gene expression variability is also heritable. Citrus species are an ideal model to accomplish the study of these questions in plants, due to the existence of varieties derived from somatic mutations that are likely to differ from each other by one or a few point mutatio ...[more]

PMID: 17452756

Similar Datasets

Transcription profiling of mouse knockouts vs wild type apoE knockout,apoA1 knockout, apoA1 transgene, apoB knockout, mice were fed normal vs artherogenic diets

Project description:Collect tissues from control C57kBL/6 and the following genetically engineered mice-apoE knockout,apoA1 knockout, apoA1 transgene, apoB knockout, LDLR knockout.Both male and female mice fed chow or atherogenic diet will be used. Animals from each group were pooled into 2 pools, one containing 4 mice and the other containing 5 mice

2010-10-10 | E-TIGR-110 | biostudies-arrayexpress

Endogenous Cell Type-Specific DISC1 Interactomes Reveal Protein Networks Associated to Neurodevelopmental Disorders

Project description:Disrupted in schizophrenia 1 (DISC1) has been implicated in contributing to a number of psychiatric diseases and neurodevelopmental phenotypes such as the proliferation and differentiation of neural progenitor cells. While there has been significant effort directed towards understanding the function of DISC1 through the determination of its protein-protein interactions within an in-vitro setting, endogenous interactions involving DISC1 within a cell-type specific setting relevant to neural development remain unclear.

2018-07-04 | PXD007103 | Pride

Global Proteomics Profiling of LPS Stimulated IMM cells

Project description:Immortalized mouse macrophages (IMMs) were stimulated with 100 ng/ml lipopolysaccharide (LPS) for 0, 30, and 60 min. The samples were analyzed using LC-MS for global proteomics.

2024-02-27 | PXD046656 | Pride

Multi-omic diagnostics of prostate cancer in the presence of benign prostatic hyperplasia

Project description:There is an unmet need for improved diagnostic testing and risk prediction for cases of prostate cancer (PCa) to improve care and reduce overtreatment of indolent disease. Here we have analysed the serum proteome and lipidome of 262 study participants by liquid chromatography-mass spectrometry, including participants with a diagnosis of PCa, benign prostatic hyperplasia (BPH), or otherwise healthy volunteers, with the aim of improving biomarker specificity. Although a two-class machine learning model was able to separate PCa from controls with sensitivity of 0.82 and specificity of 0.95, adding BPH resulted in a statistically significant decline in specificity for prostate cancer to 0.76, with half of BPH cases being misclassified by the model as PCa. A small number of biomarkers differentiating between BPH and prostate cancer were identified, including proteins in MAP Kinase pathways, as well as in lipids containing oleic acid; these may offer a route to greater specificity. These results highlight, however, that whilst there are opportunities for machine learning, these will only be achieved by use of appropriate training sets that include confounding comorbidities, especially when calculating the specificity of a test.

2024-01-26 | PXD046530 | Pride

MASH Explorer: A Universal Software Environment for Top-Down Proteomics

Project description:MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database searching algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.

2021-09-09 | PXD020615 | Pride

Synaptic GAP and GEF Complexes Cluster Proteins Essential for GTP Signaling

Project description:GTPase-activating proteins (GAPs) and guanine exchange factors (GEFs) play essential roles in regulating the activity of small GTPases. Several GAPs and GEFs have been shown to be present at the postsynaptic density (PSD) within excitatory glutamatergic neurons and regulate the activity of glutamate receptors. However, it is not known how synaptic GAP and GEF proteins are organized within the PSD signaling machinery, if they have overlapping interaction networks, or if they associate with proteins implicated in contributing to psychiatric disease. Here, we determine the interactomes of three interacting GAP/GEF proteins at the PSD, including the RasGAP Syngap1, the ArfGAP Agap2, and the RhoGEF Kalirin. We describe the functional properties of each interactome and show that these GAP/GEF proteins are highly associated with and cluster other proteins directly involved in GTPase signaling mechanisms. We also utilize Agap2 as an example of GAP/GEFs localized within multiple neuronal compartments and determine additional interactions involving Agap2 outside of the PSD. Functional analysis of PSD and non-PSD interactomes illustrates both common and unique functions of Agap2 determined by its subcellular location.

2022-02-22 | PXD006326 | Pride

The beta-catenin interactome in a vascular smooth muscle cell model

Project description:Canonical Wnt/β-catenin signalling is an essential regulator of various cellular functions throughout development and adulthood. Aberrant Wnt/β-catenin signalling also contributes to various pathologies including cancer, necessitating an understanding of cell context dependent mechanisms regulating this pathway. Since protein-protein interactions underpin β-catenin function and localization, we sought to identify novel β-catenin interacting partners by affinity purification coupled with tandem mass spectrometry in vascular smooth muscle cells (VSMCs), where β-catenin is involved in both physiological and pathological control of cell proliferation. Here, we report novel components of the VSMC β-catenin interactome.

2018-10-25 | PXD010421 | Pride

Identifying the glycoproteome of Burkholderia cenocepacia following knockdown of glycosylation using CRISPR interference (low dCas9 induction) - loading control for glycopeptide enrichment

Project description:To interrogate the glycoproteome following knockdown of pglL and subsequent knockdown of glycosylation in Burkholderia cenocepacia through Zwitterionic Hydrophilic Interaction Liquid Chromatography (ZIC-HILIC) glycopeptide enrichment with 0.1% rhamnose for dCas9 induction– loading control pre-enrichment. Using strains harbouring the pglL-targeting guide C (Bc-pglL-C) and guideless plasmids.

2023-03-20 | PXD038044 | Pride

Identifying the glycoproteome of Burkholderia thailandensis following knockdown of glycosylation using CRISPR interference - loading control for glycopeptide enrichment

Project description:To interrogate the glycoproteome following knockdown of pglL and subsequent knockdown of glycosylation in Burkholderia thailandensis through Zwitterionic Hydrophilic Interaction Liquid Chromatography (ZIC-HILIC) glycopeptide enrichment – loading control pre-enrichment

2023-03-20 | PXD037748 | Pride

Identifying the glycoproteome of Burkholderia cenocepacia following knockdown of glycosylation using CRISPR interference - loading control for glycopeptide enrichment

2023-03-20 | PXD037749 | Pride